c_cpp/etc/KaKs_Calculator/src/KaKs.h

   1 /************************************************************
   2 * Copyright (c) 2005, BGI of Chinese Academy of Sciences
   3 * All rights reserved.
   4
   5 * Filename: KaKs.h
   6 * Abstract: Declaration of KAKS class including several methods.
   7
   8 * Version: 1.0
   9 * Author: Zhang Zhang  (zhanghzhang@genomics.org.cn)
  10 * Date: Feb.2, 2005
  11
  12 *************************************************************/
  13 #if !defined(KAKS_H)
  14 #define  KAKS_H
  15
  16 #include "base.h"
  17 #include "NG86.h"
  18 #include "LWL85.h"
  19 #include "LPB93.h"
  20 #include "GY94.h"
  21 #include "YN00.h"
  22 #include "MYN.h"
  23 #include "MSMA.h"
  24
  25 using namespace std;
  26
  27 /* KAKS class */
  28 class KAKS: public Base {
  29
  30 public:
  31         KAKS();
  32         ~KAKS();
  33
  34         /* Main function to call kaks's methods */
  35         bool Run(int argc, const char* argv[]);
  36         /* Read and Calculate seq, called in "Run" main function */
  37         bool ReadCalculateSeq(string filename);
  38
  39         /* Initialize class, ready for running */
  40         int Initialize();
  41         /* Unitialize class, for unloading */
  42         int Uninitialize();
  43
  44 protected:
  45         /* Use several methods to calculate ka/ks */
  46         bool calculateKaKs();
  47         /* Show help information */
  48         void helpInfo();
  49
  50         /* NONE: an in-house algorithm in BGI, that is NG86 without correction */
  51         void start_NONE();
  52         /* NG86 */
  53         void start_NG86();
  54         /* LWL85 */
  55         void start_LWL85();
  56         /* Modified LWL85 */
  57         void start_MLWL85();
  58         /* LPB93 */
  59         void start_LPB93();
  60         /* Modified LPB93 */
  61         void start_MLPB93();
  62         /* GY94 */
  63         void start_GY94();
  64         /* YN00 */
  65         void start_YN00();
  66         /* MYN */
  67         void start_MYN();
  68         /* Model Selection and Model Averaging */
  69         void start_MSMA();
  70
  71
  72         /* Get GCC of entire sequences and of three codon positions */
  73         void getGCContent(string str);
  74         /* Check the sequence whether is valid or not */
  75         bool checkValid(string name, string str1, string str2);
  76         /* Parse the input parameters */
  77         bool parseParameter(int argc, const char* argv[]);
  78         /* Show input parameters' information on screen */
  79         void showParaInfo();
  80         /* Get title information for writing into file */
  81         string getTitleInfo();
  82
  83 public:
  84         /* Methods' name and reference */
  85         vector<string> method_name;
  86         vector<string> method_ref;
  87
  88         /* Parameters' title in outputing file */
  89         vector<string> titleInfo;
  90
  91         /* Results for windows parser that shows results on ListCtrl */
  92         string result4Win;
  93
  94         /* File name for output */
  95         string output_filename;
  96         /* Sequence file name */
  97         string seq_filename;
  98
  99         /* Flag for whether to run NG86, MLWL85, MLPB93, GY94, YN00, MYN, MS/A=model selection/averaging */
 100         bool none, ng86, lwl85, lpb93, yn00, mlwl85, mlpb93, gy94, myn, ms, ma;
 101         /* Number of compared pairwise sequences */
 102         unsigned long number;   //Maybe too many
 103
 104 protected:
 105         /* File name for detailed results for model selection */
 106         string detail_filename;
 107         /* Detailed results */
 108         string details;
 109
 110 private:
 111         /* The temporary results for write into file */
 112         string result;
 113         /* Output stream */
 114         ofstream os;
 115         /* A pair of sequence */
 116         string seq1, seq2;
 117 };
 118
 119 #endif
 120
 121
 122